[2024-10-31 04:13:53,448] multiqc [DEBUG ] No MultiQC config found: /share/apps/multiqc/1.9/lib/python3.8/site-packages/multiqc_config.yaml [2024-10-31 04:13:53,448] multiqc [DEBUG ] No MultiQC config found: /home/gencore/.multiqc_config.yaml [2024-10-31 04:13:53,448] multiqc [DEBUG ] No MultiQC config found: multiqc_config.yaml [2024-10-31 04:13:53,451] multiqc [DEBUG ] Loading config settings from: /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml [2024-10-31 04:13:53,451] multiqc [DEBUG ] New config 'report_section_order': {'general_stats': {'order': 1000}, 'demux_report': {'order': 900}, 'demux_report-1': {'order': 900}, 'demux_report-2': {'order': 900}, 'undetermined_barcodes': {'order': 800}, 'run_stats': {'order': 700}, 'fastqc': {'order': 500}} [2024-10-31 04:13:53,451] multiqc [DEBUG ] Command used: /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-31 04:13:53,486] multiqc [DEBUG ] Could not connect to multiqc.info for version check: [2024-10-31 04:13:53,486] multiqc [INFO ] This is MultiQC v1.9 [2024-10-31 04:13:53,486] multiqc [DEBUG ] Command : /share/apps/multiqc/1.9/bin/multiqc -f -c /home/gencore/SCRIPTS/GENEFLOW/bin/mqc_config.yaml . [2024-10-31 04:13:53,486] multiqc [DEBUG ] Working dir : /scratch/gencore/GENEFLOW/work/nf/85/61dcf97d79d1681381cc4eb4f3dba1/merged [2024-10-31 04:13:53,486] multiqc [INFO ] Template : default [2024-10-31 04:13:53,486] multiqc [DEBUG ] Running Python 3.8.6 (default, Oct 11 2020, 20:34:31) [GCC Intel(R) C++ gcc 8.3.1 mode] [2024-10-31 04:13:53,487] multiqc [INFO ] Searching : /scratch/gencore/GENEFLOW/work/nf/85/61dcf97d79d1681381cc4eb4f3dba1/merged [2024-10-31 04:13:53,487] multiqc [DEBUG ] Analysing modules: custom_content, conpair, peddy, somalier, methylQA, mosdepth, phantompeakqualtools, qualimap, preseq, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, goleft_indexcov, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, homer, macs2, theta2, snpeff, gatk, htseq, bcftools, featureCounts, fgbio, dragen, dedup, damageprofiler, biobambam2, mtnucratio, picard, prokka, samblaster, samtools, sexdeterrmine, bamtools, jellyfish, vcftools, longranger, stacks, varscan2, bbmap, bismark, biscuit, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, snpsplit, kat, leehom, adapterRemoval, clipandmerge, cutadapt, flexbar, kaiju, kraken, malt, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, pycoqc, minionqc, multivcfanalyzer, clusterflow, bcl2fastq, interop, ivar, flash, seqyclean [2024-10-31 04:13:53,487] multiqc [DEBUG ] Using temporary directory for creating report: /state/partition1/job-52843626/tmp49n7mtix [2024-10-31 04:13:53,597] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_3_b_fastqc.html [2024-10-31 04:13:53,600] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_3_b_fastqc.html [2024-10-31 04:13:53,650] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: 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H255JDMX2_n01_so_a_3_d_fastqc.html [2024-10-31 04:13:54,954] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_3_d_fastqc.html [2024-10-31 04:13:55,000] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H255JDMX2_n01_so_f_c_a_fastqc.html [2024-10-31 04:13:55,002] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_f_c_a_fastqc.html [2024-10-31 04:13:55,048] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H255JDMX2_n01_so_g_3_b_fastqc.html [2024-10-31 04:13:55,050] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_g_3_b_fastqc.html [2024-10-31 04:13:55,097] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_3_a_fastqc.html [2024-10-31 04:13:55,099] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_3_a_fastqc.html [2024-10-31 04:13:55,144] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_7_c_fastqc.html [2024-10-31 04:13:55,146] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_7_c_fastqc.html [2024-10-31 04:13:55,192] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H255JDMX2_n01_so_g_c_d_fastqc.html [2024-10-31 04:13:55,194] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_g_c_d_fastqc.html [2024-10-31 04:13:55,240] multiqc [DEBUG ] File ignored by hicexplorer because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_3_e_fastqc.html [2024-10-31 04:13:55,242] multiqc [DEBUG ] File ignored by longranger/invocation because it exceeded search pattern filesize limit: H255JDMX2_n01_so_a_3_e_fastqc.html [2024-10-31 04:13:55,718] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-31 04:13:55,720] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.3.2 [2024-10-31 04:13:55,728] multiqc.modules.custom_content.custom_content [INFO ] run_stats: Found 1 samples (table) [2024-10-31 04:13:55,745] multiqc.modules.custom_content.custom_content [INFO ] demux_report: Found 35 samples (table) [2024-10-31 04:13:55,754] multiqc.modules.custom_content.custom_content [INFO ] undetermined_barcodes: Found 20 samples (table) [2024-10-31 04:13:55,760] multiqc [DEBUG ] No samples found: conpair [2024-10-31 04:13:55,766] multiqc [DEBUG ] No samples found: peddy [2024-10-31 04:13:55,772] multiqc [DEBUG ] No samples found: somalier [2024-10-31 04:13:55,778] multiqc [DEBUG ] No samples found: methylQA [2024-10-31 04:13:55,787] multiqc [DEBUG ] No samples found: mosdepth [2024-10-31 04:13:55,792] multiqc [DEBUG ] No samples found: phantompeakqualtools [2024-10-31 04:13:55,796] multiqc [DEBUG ] No samples found: qualimap [2024-10-31 04:13:55,802] multiqc [DEBUG ] No samples found: preseq [2024-10-31 04:13:55,807] multiqc [DEBUG ] No samples found: quast [2024-10-31 04:13:55,815] multiqc [DEBUG ] No samples found: qorts [2024-10-31 04:13:55,825] multiqc [DEBUG ] No samples found: rna_seqc [2024-10-31 04:13:55,830] multiqc [DEBUG ] No samples found: rockhopper [2024-10-31 04:13:55,836] multiqc [DEBUG ] No samples found: rsem [2024-10-31 04:13:55,850] multiqc [DEBUG ] No samples found: rseqc [2024-10-31 04:13:55,856] multiqc [DEBUG ] No samples found: busco [2024-10-31 04:13:55,862] multiqc [DEBUG ] No samples found: goleft_indexcov [2024-10-31 04:13:55,868] multiqc [DEBUG ] No samples found: disambiguate [2024-10-31 04:13:55,874] multiqc [DEBUG ] No samples found: supernova [2024-10-31 04:13:55,889] multiqc [DEBUG ] No samples found: deeptools [2024-10-31 04:13:55,895] multiqc [DEBUG ] No samples found: sargasso [2024-10-31 04:13:55,901] multiqc [DEBUG ] No samples found: verifybamid [2024-10-31 04:13:55,907] multiqc [DEBUG ] No samples found: mirtrace [2024-10-31 04:13:55,912] multiqc [DEBUG ] No samples found: happy [2024-10-31 04:13:55,918] multiqc [DEBUG ] No samples found: mirtop [2024-10-31 04:13:55,925] multiqc [DEBUG ] No samples found: homer [2024-10-31 04:13:55,931] multiqc [DEBUG ] No samples found: macs2 [2024-10-31 04:13:55,936] multiqc [DEBUG ] No samples found: theta2 [2024-10-31 04:13:55,942] multiqc [DEBUG ] No samples found: snpeff [2024-10-31 04:13:55,950] multiqc [DEBUG ] No samples found: gatk [2024-10-31 04:13:55,955] multiqc [DEBUG ] No samples found: htseq [2024-10-31 04:13:55,962] multiqc [DEBUG ] No samples found: bcftools [2024-10-31 04:13:55,967] multiqc [DEBUG ] No samples found: featureCounts [2024-10-31 04:13:55,975] multiqc [DEBUG ] No samples found: fgbio [2024-10-31 04:13:55,990] multiqc [DEBUG ] No samples found: dragen [2024-10-31 04:13:55,995] multiqc [DEBUG ] No samples found: dedup [2024-10-31 04:13:56,000] multiqc [DEBUG ] No samples found: damageprofiler [2024-10-31 04:13:56,028] multiqc [DEBUG ] No samples found: biobambam2 [2024-10-31 04:13:56,032] multiqc [DEBUG ] No samples found: mtnucratio [2024-10-31 04:13:56,035] multiqc [DEBUG ] No samples found: picard [2024-10-31 04:13:56,040] multiqc [DEBUG ] No samples found: prokka [2024-10-31 04:13:56,045] multiqc [DEBUG ] No samples found: samblaster [2024-10-31 04:13:56,055] multiqc [DEBUG ] No samples found: samtools [2024-10-31 04:13:56,060] multiqc [DEBUG ] No samples found: sexdeterrmine [2024-10-31 04:13:56,066] multiqc [DEBUG ] No samples found: bamtools [2024-10-31 04:13:56,071] multiqc [DEBUG ] No samples found: jellyfish [2024-10-31 04:13:56,080] multiqc [DEBUG ] No samples found: vcftools [2024-10-31 04:13:56,086] multiqc [DEBUG ] No samples found: longranger [2024-10-31 04:13:56,092] multiqc [DEBUG ] No samples found: stacks [2024-10-31 04:13:56,097] multiqc [DEBUG ] No samples found: varscan2 [2024-10-31 04:13:56,115] multiqc [DEBUG ] No samples found: bbmap [2024-10-31 04:13:56,120] multiqc [DEBUG ] No samples found: bismark [2024-10-31 04:13:56,126] multiqc [DEBUG ] No samples found: biscuit [2024-10-31 04:13:56,132] multiqc [DEBUG ] No samples found: hicexplorer [2024-10-31 04:13:56,137] multiqc [DEBUG ] No samples found: hicup [2024-10-31 04:13:56,143] multiqc [DEBUG ] No samples found: hicpro [2024-10-31 04:13:56,147] multiqc [DEBUG ] No samples found: salmon [2024-10-31 04:13:56,153] multiqc [DEBUG ] No samples found: kallisto [2024-10-31 04:13:56,158] multiqc [DEBUG ] No samples found: slamdunk [2024-10-31 04:13:56,164] multiqc [DEBUG ] No samples found: star [2024-10-31 04:13:56,169] multiqc [DEBUG ] No samples found: hisat2 [2024-10-31 04:13:56,174] multiqc [DEBUG ] No samples found: tophat [2024-10-31 04:13:56,179] multiqc [DEBUG ] No samples found: bowtie2 [2024-10-31 04:13:56,184] multiqc [DEBUG ] No samples found: bowtie1 [2024-10-31 04:13:56,190] multiqc [DEBUG ] No samples found: snpsplit [2024-10-31 04:13:56,195] multiqc [DEBUG ] No samples found: kat [2024-10-31 04:13:56,200] multiqc [DEBUG ] No samples found: leehom [2024-10-31 04:13:56,206] multiqc [DEBUG ] No samples found: adapterRemoval [2024-10-31 04:13:56,210] multiqc [DEBUG ] No samples found: clipandmerge [2024-10-31 04:13:56,215] multiqc [DEBUG ] No samples found: cutadapt [2024-10-31 04:13:56,221] multiqc [DEBUG ] No samples found: flexbar [2024-10-31 04:13:56,226] multiqc [DEBUG ] No samples found: kaiju [2024-10-31 04:13:56,232] multiqc [DEBUG ] No samples found: kraken [2024-10-31 04:13:56,237] multiqc [DEBUG ] No samples found: malt [2024-10-31 04:13:56,242] multiqc [DEBUG ] No samples found: trimmomatic [2024-10-31 04:13:56,247] multiqc [DEBUG ] No samples found: sickle [2024-10-31 04:13:56,252] multiqc [DEBUG ] No samples found: skewer [2024-10-31 04:13:56,258] multiqc [DEBUG ] No samples found: sortmerna [2024-10-31 04:13:56,263] multiqc [DEBUG ] No samples found: biobloomtools [2024-10-31 04:13:56,268] multiqc [DEBUG ] No samples found: fastq_screen [2024-10-31 04:13:56,274] multiqc [DEBUG ] No samples found: afterqc [2024-10-31 04:13:56,279] multiqc [DEBUG ] No samples found: fastp [2024-10-31 04:14:01,321] multiqc.modules.fastqc.fastqc [INFO ] Found 35 reports [2024-10-31 04:14:01,846] multiqc [DEBUG ] No samples found: pycoqc [2024-10-31 04:14:01,851] multiqc [DEBUG ] No samples found: minionqc [2024-10-31 04:14:01,856] multiqc [DEBUG ] No samples found: multivcfanalyzer [2024-10-31 04:14:01,862] multiqc [DEBUG ] No samples found: clusterflow [2024-10-31 04:14:01,867] multiqc [DEBUG ] No samples found: bcl2fastq [2024-10-31 04:14:01,873] multiqc [DEBUG ] No samples found: interop [2024-10-31 04:14:01,878] multiqc [DEBUG ] No samples found: ivar [2024-10-31 04:14:01,883] multiqc [DEBUG ] No samples found: flash [2024-10-31 04:14:01,888] multiqc [DEBUG ] No samples found: seqyclean [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Demultiplexing Report'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Demultiplexing Report'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Demultiplexing Report'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Demultiplexing Report'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Demultiplexing Report'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Demultiplexing Report'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module ' Barcodes of Undetermined Reads'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module ' Barcodes of Undetermined Reads'. [2024-10-31 04:14:01,888] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module ' Barcodes of Undetermined Reads'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module ' Barcodes of Undetermined Reads'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module ' Barcodes of Undetermined Reads'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module ' Barcodes of Undetermined Reads'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'Run Statistics'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'Run Statistics'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'Run Statistics'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'Run Statistics'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'Run Statistics'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'Run Statistics'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'Run Statistics'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'general_stats' not found for module 'FastQC'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'demux_report' not found for module 'FastQC'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-1' not found for module 'FastQC'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'demux_report-2' not found for module 'FastQC'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'undetermined_barcodes' not found for module 'FastQC'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'run_stats' not found for module 'FastQC'. [2024-10-31 04:14:01,889] multiqc [DEBUG ] Reordering sections: anchor 'fastqc' not found for module 'FastQC'. [2024-10-31 04:14:01,930] multiqc [INFO ] Compressing plot data [2024-10-31 04:14:02,603] multiqc [INFO ] Report : multiqc_report.html [2024-10-31 04:14:02,603] multiqc [INFO ] Data : multiqc_data [2024-10-31 04:14:02,603] multiqc [DEBUG ] Moving data file from '/state/partition1/job-52843626/tmp49n7mtix/multiqc_data' to '/scratch/gencore/GENEFLOW/work/nf/85/61dcf97d79d1681381cc4eb4f3dba1/merged/multiqc_data' [2024-10-31 04:14:02,739] multiqc [INFO ] MultiQC complete